In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples

Jan Hejátko, Ikram Blilou, Philip B. Brewer, Jiří Friml, Ben Scheres, Eva Benková

Research output: Contribution to journalArticlepeer-review

123 Scopus citations


High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used.

Original languageEnglish (US)
Pages (from-to)1939-1946
Number of pages8
JournalNature Protocols
Issue number4
StatePublished - Nov 2006
Externally publishedYes

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology


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